mmg_233_2013_genetics_genomicswikiaorg-20200214-history
Bioprospecting in Cow Rumen
Here is a riddle for you: What do gold and cows have in common? The answer: They both grab the attention of prospectors! Maybe the "Forty-Niners" of the California Gold Rush are not exactly like the bioprospecting scientists of today, but the mentality is the same. Both were looking for something useful in nature. In the case of bioprospecting, those useful things are not necessarily as tangible as gold. Today, scientists are looking heavily into molecules and enzymes used by microbes in the hope of repurposing them and using them to help out society. One particularly interesting case of bioprospecting comes from a group at the Joint Genome Institute, where Matthias Hess and coleagues used metagenomics to help identify enzymes from microbes in the cow rumen that could be used to help make biofuels from plant material. Biofuels Biofuels are considered to be an important and renewable energy source that is made from plant matter, which is either grown for the purpose of making biofuels or is obtained as a by-product of crop harvesting (1 , 2 ). Biofuels can be an alternative to fossil fuels in different areas of use, such as trasnportation (1 ). While biofuels are not necessarily "clean" energy, the usefulness lies in the fact that they are a renewable energy source, since new plant material can be grown as other plant material is harvested to make the fuels (2 ). The obstacle preventing a large-scale production of biofuels is the lack of an efficient way to create those fuels from cellulose (1 ). This is where bioprospecting can help. Bioprospecting Bioprospecting is looking for useful products or processes in nature, typically through scientific research (3 ). In the case of this study, the researchers were looking for enzymes that could break down cellulose to make biofuels. To do this, they decided to look to the rumen of a cow, were plant matter (and therefore cellulose) is constantly being broken down. By incubating switchgrass (which can be used to make biofuels) in the rumen of a cow, the researchers could collect microbes that would grow on the switchgrass and break down the cellulose in the grass. A metagenomic analysis of the microbes on the switchgrass was then used to identify candidate genes responsible for the hydrolysis of cellulose (1 ). Metagenomic Analysis To find potential enzymes that can break down cellulose, the researchers took a sample of microbes from the incubated switchgrass and sequenced the DNA. This resulted in a total of 268 Gbp, out of which about 2.5 million open reading frames were predicted. Of these open reading frames, 27,755 genes were predicted to code for carbohydrate-active enzymes based on a sequence similarity to at least one catalytic or carbohydrate-binding domain. After sequence comparisons of the predicted genes to known carbohydrate hydrolyzing enzymes, 90 genes with a predicted glycoside hydrolase or carbohydrate-binding domain were chosen for functional analysis. These enzymes were tested for activity of 10 different substrates, resulting in 51 enzymatically active candidate enzymes (1 ). These enzymes could be studied further for usefulness in industrial-scale biofuel production. References 1. Hess, M. et al. Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen. Science. 2011 2. Biofuels. New York State Department of Envrionmental Conservation. 3. What is Bioprospecting? National Park Service.